The Missing Molly Hooper Files
by Writingwife83
Summary: This is a look at series 1-3 with me adding in what I WISH had been there involving Sherlock and Molly. There were lots of times I felt like Molly should have gotten more screen time or more detail than she did, so I decided to fill in some blanks. My goal was to turn this into a slow progress to the start of something more for Sherlolly by the end of series 3. Please review!
1. Series 1 Ep 1

Molly couldn't think fast enough to say anything else before he left the room. She had said "okay" and that was all, but he probably didn't even hear that. He'd been halfway out the door by the time she'd said it. She began hurrying around putting things away and clearing out the usual evidence that Sherlock Holmes had been in the morgue. Not that most people weren't well aware and turned a blind eye. She felt she needed to hurry now though. He'd said he'd be upstairs. What if she was slow and he left before she got there?

She was actually stifling a grin because she felt a little proud of herself. There had been many days over the past couple of years that she'd looked herself in the mirror and said, "today I'll do it. If Sherlock comes in today, I'll ask him out." But thus far it hadn't happened. He was either too quick about his business for conversation of any kind, or he'd say something thoughtless and she'd get discouraged. But today she'd actually done it! And he said yes...sort of. Well not really, but he didn't say no. Surely he'd at least sit with her while he had his coffee, seeing as she had invited him. But even as she tried to reassure herself, she realized that Sherlock didn't hold to those sort of rules of conduct. It was highly unlikely that he'd do more than take the coffee from her hand, say thank you, and be on his way.

By the time Molly left the morgue, she was feeling down again. Somehow the high of asking Sherlock to have coffee had been whisked away briskly by her own mind. She chastised herself for allowing hope to grow even briefly. As she boarded the elevator she began to think she shouldn't have even asked in the first place. A couple of her close friends had strictly instructed her not to ask Sherlock out.

_"Molly, he's known you for more than two years. If he hasn't asked you out by now, he's not going to," one had said._

_"You're into science, you know this stuff! Don't take it personally. It's all chemical! You're probably not giving off the right chemicals for him and he will never be attracted to you, no matter how pretty you are," another had said._

_"You already look desperate for his attention. Do not make it worse and make the first move."_

All these well meaning pieces of advice fell on deaf ears, for the most part. She really didn't care what anyone else thought of Sherlock or how he treated her. It was only after she did something she really regretted that these special tidbits of advice would flood back into her head. Didn't happen often since usually she did nothing to merit any regret with Sherlock. He didn't allow much leeway for that.

Molly went to the cafeteria and got the coffee with a stony expression. She resolved to take the coffee to Sherlock in the lab, hand it over, and be the one to walk away quickly. She had no need to be there at the moment. Just give him the coffee and leave. No need to give him the opportunity to be rude or indifferent. She decided she should be the indifferent one this time.

Molly got to the lab and felt her heart betraying her already. Sherlock was putting something into a dish and leaning over to look closely at it on the table. The perfect fit of his white shirt and dress pants made him look more like he was posing for a photo shoot than doing an experiment. She took a deep breath and tried to envision herself being completely disinterested and setting the coffee down with barely a word. She stepped in briskly.

"Here you are, Sherlock. Black, two sugars." She set the cup down. "I'll be going now then." She began to turn to head back the way she came.

"You're off rather quickly Molly," he stated without looking up.

She stopped and turned around again. "Oh, did you need me to stay? I can stay if you'd like."

"What would I need you to stay for?"

Just like that, her plan of action had been squashed. She'd, once again, turned into the one hoping for attention and he was he one who didn't care.

"Well, I don't know...you seemed to be asking-" she began.

"I was simply confused at why you were rushing off since you're clearly done for the day. You have your list folded up in your lab coat pocket. You only do that at the end of your day. You take it off your clip board and fold it up, putting it in your pocket to drop on your managers desk on the way out. So I imagine you're not exactly in a rush to get back to work. And besides, you never rush off even if you do have a full list to attend to."

"Well, maybe I'd just like to get home."

"To your cat?"

She looked around a little embarrassed and folded her arms protectively in front of her. "Yes...to my cat."

"Right...well don't let me keep you. Thanks for the coffee, Molly." He barely looked up at her before returning his gaze to the counter and his work.

"Sure...see you later, Sherlock." Molly pressed her lips together while walking out of the lab. How had that happened? she wondered. Somehow she still managed to come out of there feeling like he couldn't care less whether she existed or not. Unless of course he needed her to do something for her.

And if she was honest with herself, she was already foolishly looking forward to the next time he did.


	2. Series 1 Ep 3

Molly hopped in a cab and tried to dry her eyes as she did so. She was too upset to think straight, and what she was doing was stupid. She knew that, but she had to do it. What she'd just heard and seen had scared her, and she didn't know what else to do except to see him.

She had just seen on the news that there had been a confrontation with wanted criminal Jim Moriarty and famous consulting detective Sherlock Holmes. The incident was over, and the criminal had escaped. Sherlock Holmes was also said to be alive. What had really merited her horror was the fact that there had now been a picture released of this criminal mastermind...Jim...Jim from IT upstairs...Jim who had been so enthralled with everything she said about Sherlock...Jim who she had briefly gone out with...

Molly had tried calling Lestrade, but he wasn't answering. She boldly decided to go to 221B Baker Street. She wanted to see Sherlock, hear his voice, and make sure that he was truly safe. She had some strange sense of responsibility. She replayed the day not long before when she had introduced Jim to Sherlock. It had been a horrible thing anyway, but now the memory almost made her sick. He wanted to get to Sherlock, in any way he could, and he saw the opportunity through her. She knew that Sherlock had apparently made it out alive, but even the idea that he could have been hurt or killed because of a man that she had introduced him to him was extremely troubling.

She arrived at their apartment building, and by this time it was past ten at night. She wanted to leave right after she'd climbed out of the cab and it drove away, but she was there, and it would feel even worse to leave now without having seen Sherlock at all. She climbed the stairs and knocked a little hesitantly. Not surprisingly to her, John came to the door.

"Molly, hello...I didn't know you were coming over," he said, nicely trying to figure out her presence.

"Neither did I. I mean, I didn't plan to really. I just had to stop quickly by and uh..."

John peered at Molly a little in the doorway. "Molly, are you ok? Oh, Molly...you saw the news didn't you? And they showed a picture of him...I'm sorry, we should have called you."

"No no! That's silly really. You didn't have time for any of that. I just got worried when I heard the report, and wanted to make sure things were really ok. You're ok, right? You're...both ok?" Her eyes darted conspicuously into the apartment past John.

"Well, come in Molly, you can talk to Sherlock yourself." John ushered her in and encouraged her to have a seat on the couch. "He's been holed up in his room for the past couple of hours, so it's time to pry him out anyway. I'll be right back."

Molly had never felt so awkward in all her life. She sat there on the couch and thought about the fact that Sherlock surely didn't enjoy unannounced visitors, and especially not when he was preoccupied with a case...a dangerous one too. She wondered what she imagined he'd say to her. He would end up making her feel like a fool again, and she'd wish she'd never come.

"Molly," his deep voice said as he entered the living room.

He wore cotton pants for sleeping and what looked like a white tee shirt beneath a dark blue dressing gown. She'd never seen him in anything other than his dress pants and button down shirts. The sight of him like this altered her perception of him a little. He was actually a regular man sometimes. A man who didn't always look impeccably dressed. He wore his robe around his apartment, just like she remembered her father doing on evenings and Sundays. And a question was answered then in her mind. She had often wondered if her feelings for Sherlock Holmes would change should she see him beyond the clever, handsome, put together man who liked to stop by the hospital. The truth was that it did change things. She fell much more deeply in love with him.

"Is there a problem?" he continued, and walked over to take a seat in his chair by the fire.

"No-not really. Just saw the news and well...I had to make sure you were both ok," she said, fiddling with the zipper on her jacket.

"I do seem to be in one piece. Moriarty is, although extremely clever, not quite able to best me yet. He'll surely be back though. He made it clear he wasn't done with me."

"I just hope you know I had nothing to do with- I mean, I had no idea what kind of a man he was!" she sputtered out. "I'd never have gone out with him, and I'd certainly never have let him meet you!"

Sherlock frowned in his typical fashion, making her feel that she was being silly.

"Molly, please, of course you have no idea! He made sure you wouldn't. He's clever, and he knew how to make you sure that he liked you. He would have been good at playing a part. He fooled me as well, truly. I couldn't see past his false exterior to deduce him as he actually was. That's a feat not many can say they've accomplished."

"It just makes me sick," she muttered "that he tried to hurt you...and John."

"He hates me, Molly. He's going to hate me more now, of course. He'll keep coming back for me because it's a game to him. It's not even about killing me. It's a battle of wits, and he wants to be better than me."

"He'll never be as clever as you." The words sounded a little more endearing than she'd meant it to. She noticed Sherlock's eyes narrow against her as he clearly tried to analyze the tone of her voice. She could tell it had him a little perplexed. There were some things that Sherlock couldn't figure out so easily, and they all seemed to be things related to the heart.

"Why are you here, Molly?" he asked, almost suspiciously.

"Well, I...I was worried. Just showing some, you know, friendly concern. We're friends...aren't we Sherlock?" She could see him processing this question. She'd never known him to have lots of friends. But he did seem to be awfully friendly with John Watson, who was now living and working with him. She couldn't imagine that he didn't consider her a friend, having known her and worked with her for more than two years now.

He got up and stood by the window staring outside briefly before turning and answering. "Yes, Molly. We can be...friends, if you'd like." The statement appeared to taste funny in his mouth, the words being strange and unfamiliar on his tongue. He stood there with his hands clasped behind him, looking unsure of what to do or say next. She knew he wasn't interested in her staying any longer, so she decided to put him out of his misery.

"Well, I'll be going then. I'm glad you're both alright." She stood up as she spoke, moving toward the door.

Sherlock did walk over a little closer to the door as she opened it and stood on its threshold, still seeming uneasy at the idea of saying goodbye to a visitor who had come over claiming to be his friend. "Oh and John said to tell you goodnight. He went to his room after he got me. Seemed to have the idea you were just here to speak to me." There was something in the way he said it. It was almost a question. Almost as if he was testing her, trying to figure things out himself. He was still perplexed by the idea of a woman coming all the way over to his apartment at night just for the purpose of seeing him and finding that he was alright.

"Really? Oh." Molly gave a small nervous laugh. "Well, tell him goodnight for me then."

"Goodnight, Molly Hooper," he said, with a half smile.

"Yes, goodnight," she said as she left, and heard the door close once her back was turned. She couldn't help but think that this hadn't gone quite as badly as she'd feared it would...


	3. Series 2 Ep 1

Molly had looked at herself in the mirror and agonized before leaving her flat. She didn't want to appear desperate, but she did want to send some sort of a message to Sherlock. Things had been going pretty well for a while, and she felt like he could use a reminder that she was actually a woman, and she was attracted to him. She had been more than thrilled when he had come in last week to the hospital and mentioned in passing that she could come over for a small Christmas party if she'd like.

The dress, the hair, and the makeup could be too much...but she had felt confident she looked good, and she hoped that it would be enough to at least make Sherlock take a second glance. All he ever usually saw her in was a big white lab coat, and that certainly would never put ideas in a mans head. This, on the other hand, could have.

Could have...but didn't. An hour later, Molly wasn't only regretting her choice of outfit, but was also regretting even coming out tonight. The horror of Sherlock's most painful deduction of her yet hung in the air and everyone looked just as embarrassed as she was. Molly spoke to herself, more so than to Sherlock when she finally managed to push words out.

"You always say such horrible thing. Every time. Always...always..." In saying this, she was really questioning herself. Asking herself why. Why did she love this man who made her feel so terribly small and silly and undesirable? He did always say horrible things. How many horrible things would it take for her to stop him from invading her heart and find him repulsive instead of irresistible? She was as much at fault as he was, more so perhaps. He barely knew what he did when he spoke to her. He spoke to her in the same way he did to everyone else. She, on the other hand, was fully aware and yet kept coming back for more. She hated herself in that moment.

But then he opened his mouth again.

"I am sorry...forgive me," he said as he swallowed a breath visibly and looked down in embarrassment. "Merry Christmas, Molly Hooper."

And then he leaned down slowly and pressed a light kiss to her cheek. Her heart leaped back into the lovely bonds of hope it had barely begun to climb out of only moments before. She barely had time to think before a dreadfully embarrassing moan was heard by all. Then all she could think was to make sure nobody thought it had been her!

When Sherlock announced that it was his text alert, and John added that it was the fifty seventh he had received, Molly was crushed yet again. It was the fastest roller coaster ride of emotions she'd ever experienced in the course of two minutes.

Sherlock quickly excused himself and she immediately flopped down into the chair next to the fire.

"Sorry, Molly! You must not mind him. He's been ever so occupied with this case. It's not you my dear," Mrs. Hudson said in her sweet comforting voice.

"Molly, can I get you some more wine?" John offered.

"Yes, please, John," she said, having just consumed the rest of hers in three large gulps.

John came over and poured some into her glass and he looked at her with a pitying expression. She felt like slapping him at the moment because she didn't want pity. She wanted to be the woman who didn't need pity...the woman who seemed to command his immediate attention from a simple text. She could only assume this was a woman. She needed to know.

"John, who just sent a message to Sherlock?" she asked quietly.

John looked at her sheepishly, and glanced around him, perhaps checking to make sure Sherlock was still in him room. "She's a woman named Irene. Involved in a case Sherlock is working on. She seemed to have...an unusual effect on him. Unusual for Sherlock at least."

Molly pursed her lips and nodded slowly while peering into the wine glass. A woman who had an unusual effect on Sherlock. Her worst fears were suddenly reality. How could she compete with this? At least before, she was simply in love with a man who seemed to have no interest in any women at all. But now...she could feel her eyes stinging and there was no worse shame than to cry in front of all these people.

"John, I'm really sorry, but I think I'd like to go," she said, standing up and handing him her wine glass.

"Molly, don't go. This is Sherlock! It's what you get when you're dealing with him. I know this looks...discouraging to you. But trust me, this woman is not...just any average woman. Sherlock isn't exactly going to take her home to his mother and have her over for dinner on weekends. Maybe, at the very most, she's what he wants right now. But trust me, she is not what he needs." He looked at her intensely, trying to make her see something positive.

"I'd love to think you're right, John. But I still need to go. Thanks for the invite. And I hope the rest of your evening is a little less eventful." Molly excused herself quickly.

* * *

><p>Molly wasn't at home for long though. Not two hours later, she got a call from the hospital. A body had to be identified, and nobody else was available to come in. She was, of course. When she got there and had seen the name, and soon after saw Sherlock arrive with his brother in tow, a chill went through her...Irene. This was the woman. The woman who was able to pull Sherlock away from a room full of guests with one little message. And as Molly looked at this woman who was beaten to a pulp before she had finally died, she still envied her in a way. She'd certainly done things in her short life that Molly was beginning to think she herself would never be able to accomplish.<p>

She watched Sherlock's steely eyes as they scanned this woman's entire body confirming her identity. Molly blushed in embarrassment, despite the fact that it had nothing to do with her. It was as if she was watching something she shouldn't be allowed to see. She covered up the body again when they were through, and cleaned up quickly. Sherlock stood in the middle of the hallway outside when she came out.

"Sorry," she said quietly, walking up beside him.

"You have nothing to apologize for," he said simply.

"I meant, sorry for your loss, Sherlock."

"Ah...still, not really necessary. I barely knew her." He walked over to the wall and leaned his back against it.

"Maybe not. But, I think it was still a loss. It's ok to feel sometimes, Sherlock, you know? Even if it's silly."

"I don't know if I agree, Molly...I've felt too much tonight, and it doesn't seem at all ok to me. How do you people do it all the time?" He asked in a sort of disgusted tone.

She shook her head. "I'm not the best one to ask right now. I'd like some time off from feeling as well. Feeling can...make you crazy. You're probably saving yourself a lot of trouble."

He looked over and met her eyes for a moment in the dimly lit hallway. "I'm beginning to think I'm not very good at it anymore...not feeling, I mean. I'd probably be a lot better off if I'd never met Mrs Hudson, or John...or you."

Molly smiled ruefully. "Don't blame it on me, Sherlock. I haven't been very good at making you feel anything."

Sherlock came over closer to her and she was almost afraid for a moment, since he never usually bothered to come closer to her. "I'm not like other people, Molly. When I do feel anything, most people don't really know it. Maybe you just need to watch me a little bit closer...I'm sorry again, that I hurt you. I know I hurt you. Maybe I know now how you feel, just a little." He looked down at her, almost seeming to consider what to do next, but then he turned and began walking away.

"Goodnight, Molly." he said without looking back. He went down the hall, leaving Molly in the wake of a rare emotional moment.

"Goodnight," she whispered, much too quietly to be heard by anyone else.


	4. Series 2 Ep 3

Molly ran down the long hallway in the basement to the back of the hospital making her footsteps echo behind her as she went. She pushed her way through the morgue doors and ran to where the back entrance was. She pushed in the code to open the double doors, hands shaking a little bit.

"Hello," she breathed out quickly, and the man standing there clearly looked her over for a moment, wondering why she was out of breath. "Sorry, I was all the way upstairs." she managed a little laugh, trying to lighten the mood.

"Okay...Well here he is anyway. Just sign this," the man said, holding out the metal clipboard. She took it, and tried to stop her fingers from shaking as she signed her name.

"Thanks a bunch, and sorry for the rush. Big mix up!" she said, throwing her hands up a little in mock embarrassment. The man nodded slightly and walked back to the van, not terribly concerned. That was good. She didn't want any interest at all.

Molly pulled the gurney with the large black body bag on it up the ramp and rolled it over past where she'd normally take it. She pushed the gurney out of the morgue and past the elevators to the other end of the building, averting her eyes the couple of times she passed other staff. She got to the door and knocked three times. Then she opened it. The three "doctors" were waiting there in their lab coats. She pushed the gurney out to them and saw them lifting the body bag up and off as she shut the doors again.

It was almost a full hour later when she heard three knocks on the door and she opened up again. The men were lifting the bag back up onto the gurney. After they did they zipped it the rest of the way, as it was still opened a little. Molly then saw a glimpse of his face, and felt her stomach turn. She pulled the gurney back through the doors and rolled it quickly back to the morgue. She pushed it into the large supply closet and then locked the doors behind her. And it was done. That had been the hardest part. Now she just had to wait for Sherlock.

She paced the hallways and waited for the sounds she knew she'd hear. It was a few minutes of torture before she heard the sound of the service elevator doors opening, and the frantic rush of the wheels on the floor. She pushed the button to open the doors for them, and two more "doctors" rolled another gurney toward her. She looked behind her and past them down the hallway, then said aloud, "It's all clear."

And then he sat up. Sherlock sat up from where he lay, his face and hair covered in the sticky fake blood and dirt from the pavement. "Let's go, quickly," he said, but she heard his voice shaking a bit.

The man and woman pulled their white coats off revealing their street clothes beneath and handed them to Molly. She took them and balled them up in her arm before speaking to them. "Let yourself out the back door where I met you before. It locks behind you. Just disappear as quick as you can. His brother will take care of you later." The two of them nodded and went running back in the other direction.

"Come on," Molly said and took Sherlock by the arm into the morgue. She locked the door behind her and shut the lights off, all but one in the back.  
>She ran to the back with Sherlock following her and opened the bathroom door.<p>

"Stay in here. I just have to get the body out onto the table and set the papers where they need to be, and then I'll help you." He nodded and went in.

She went to the supply closet and wheeled "Sherlock's" body out into the main room. She took out a metal clip board that had been ready in the drawer file cabinet and lay it on top of the body bag. Then she placed a previously written note on top.

_~I can't do any more for now...I knew him, and he meant so much to me. I did the intake. But that's all I could manage, sorry. I'll be back later._

_Molly H._

But of course she had to check. Had to make sure things looked right. She slowly pulled the heavy sipper down and revealed the pale face that was familiarly haloed in dark curls. She sucked in a breath and held it for a minute before letting it out. The sight of the dead never made her ill or nervous, but this was the most sickening feeling she could ever recall. The resemblance, injuries, and marks were perfect. Too perfect for her to look at in that moment as she stood frozen. She didn't even hear Sherlock come up behind her, so she jumped a little when his hand grasped hers.

"Molly, close the bag. We can't lose any time," he said in a calm but commanding voice. She saw that he wasn't looking down on purpose, but keeping his eyes fixed on her instead. He had wiped his face and hair mostly clean already in the bathroom.

Molly carefully removed her hand from his and so that she could zip the black bag closed again, then he put a hand on her back and led her quickly back into the bathroom. She locked the door once inside and then looked at Sherlock as she rested her back on the wall. He placed his hands on the sides of the sink and let his head hang down for a moment. He took deep breaths that she could see from where she stood.

"You jumped," she said quietly.

"Yes...I jumped," he answered, with his head still down.

"Did you kill Moriarty?"

"No. But he's dead...he shot himself."

"What?!" she exclaimed in a whisper and came over closer to the sink. "My God..."

Sherlock stood up straight then and looked at himself in the mirror. He ran a hand through his hair and continued to feel residue of the fake blood. He began running some paper towels under the tap, but Molly could see his hands were shaking.

"Here, let me," she said instinctively and he didn't even object as he moved aside and she took the towels from his hands and rung them out a bit. "Look down a bit...you're tall, aren't you. I can barely see your forehead standing here in front of you."

He said nothing in protest, but bend his face down toward her for better reach. Molly hesitantly reached up and smoothed some hair back from his forehead. She wiped the red away in the places along his hair line that he'd missed before. "Turn," she said softly and he obliged so she could reach a spot behind his jaw line. His face was serious and sad. But he seemed to be calmer now.

"How much did John see?" she finally made herself ask.

"I believe John saw exactly what he needed to see, and not one bit more," he answered in a somber tone.

Molly's heart broke for him. She knew that she wasn't the person he cared most for, or was closest to. He would rather be there sharing this emotionally trying moment with someone else. John was his best friend, and she was nothing close to that. She knew he would be agonizing internally about what John was going through at this moment, having just watched his best friend leap to his death.

She pushed another section of hair back from the side of his face and continued wiping gently as she spoke again. "If you've changed your mind, you can tell me. I mean, I could always tell him, after you're gone of course. If it would make things easier-"

"No," he said immediately. "There will surely be people continuing to watch John, as well as Mrs. Hudson and Lestrade. It has to look real. And the best way to do that is to make it real...for them."

Molly bit her lower lip and nodded slowly in compliance. "Well it's fortunate that nobody's watching me then eh?. Good thing." She smiled for a brief second.

"Yes, Molly. It is a good thing...but perhaps you should make some effort to appear grieved to some degree."

She met his eyes briefly before looking back to the spots she was working to remove. "I will be, Sherlock. I wont need to pretend. You may be alive, but...you wont be here." She frowned a little, trying to control her emotions from showing through in her face.

Sherlock reached up suddenly and gently grasped her wrist to take her hand down, stopping her efforts. His eyes searched hers as he did this. "We don't have any more time, Molly...we need to go."

"Right. Well you'll just be in need of a nice shower when you get to...wherever it is you're going. I don't think any amount of paper towels will get your hair cleared of that stuff." She automatically touched his hair when she said it, but she let her hand linger for just a moment before it fell again. He didn't move right away, and seemed frozen.

"I'll go out and get the gurney and bag. Wait here." she said, breaking the moment and opening the bathroom door. She got a gurney and opened a body bag, then wheeled it back into the bathroom with her.

"Ok, climb in. Just try to relax. This wont be pleasant, I'm sure. I have the van waiting outside, but we'll still have to be fast. If anyone sees me wheeling you out..."

"They wont. You'll do fine," he said, reassuring her her as he lay down on the thick plastic. She zipped the bag up almost all the way, but left an opening for air flow.

"You ok?" she whispered afterward.

"I can't talk, Molly, I'm dead."

Molly smiled fully for the first time almost all day. "Ok, well I'll stop talking to you then...here we go."

She pushed him out the double doors and down the ramp where a van had been placed and waiting. The sixty seconds that it took her to push the gurney into the van and get in herself felt like an eternity. She finally felt she could breath normally after she started the engine and actually began driving. She got onto the road and waited a few minutes till they had gotten a little distance between them and the hospital.

"Ok, you can come out now if you want!" she called into the back, and then heard the zipper sliding and a thud as Sherlock got down off the gurney onto the floor of the van. He crawled forward so that he sat on the floor right behind the drivers drivers seat. "I hope you know where we're going, because Mycroft wouldn't tell me anything," she added.

"You'll have to forgive him. He doesn't know and trust you the way I do."

Molly had to concentrate on the road. She wanted to turn around and look at him to see his face. She hated to miss anything he was saying to her in these moments. Every word and every look he bestowed on her was one of the last, for what could be a long time. She shuddered to imagine exactly how long. He had made mention that he'd have to go away for quite a while to secretly break down Moriarty's network and bring his lies to the surface for the officials to discover more readily. But he'd given no specifics, and she had known he probably wouldn't, partly because he may not know himself.

Sherlock gave her directions as she continued to drive further out from the city. It was getting pretty dark by now, and Molly was glad. She was still terrified of any interference. She didn't know what to do if anyone discovered them.

She finally drove the van down a dirt road for a full five minutes till the road and trees opened up and she was able to see a large expanse of field. A few hundred feet away, Molly could see a car waiting, and also a small plane. She pulled up close enough to see Mycroft standing beside the car, and then shut off the engine. She jumped out and opened the back door of the van, letting Sherlock step out. He strolled over toward his brother.

"You're already behind schedule, Sherlock. I'm expected at the hospital to identify your body, and I'd rather not be late. The plane is running, and you'd better get on it. The few essentials you need are already on board." He turned toward Molly. "Your assistance has been greatly appreciated, Miss Hooper. You've been invaluable."

"Yes, she has been. In fact, could you give us a minute, Mycroft?" Sherlock said looking back and forth between his brother and Molly.

Mycroft rolled his eyes and looked at his watch again. "Do hurry up, Sherlock." And then he walked back toward the plane.

Sherlock turned then toward Molly and looked down at her. Molly thought he had had something specific to say or ask since he had requested this private moment. But now looking up at him, it seemed to her that he didn't know exactly what to say. So she decided to speak instead.

"You are coming back, Sherlock, aren't you?"

"Yes, Molly. I'll be back. Though I can't say when. It could be...a long while." He looked down at his feet.

"Well...safe travels then, wherever it is they take you. And don't stay away longer than you have-" but her words stopped short in mid breath. Sherlock had reached up and placed his hand on the side of her face. He stepped forward a little to close most of the distance between them, and she felt is thumb moving slightly over the skin on her face. He gently pulled her forward a little, then leaned down and pressed his lips to her cheek. The contact of the kiss lingered a little. Certainly more so than the apologetic kiss in his flat. When his lips released the soft skin, he kept his face where it was and hovered there cheek to cheek with her.

"Thank you," he murmured softly.

Molly felt her eyes threatening and beginning to sting, and she didn't trust her voice. All she could do was reach up and wrap her small finger around the hand that was still against her face. His fingers responded in kind, but their hands stayed pressed against her face for a moment. Then he slipped his hand out of hers, and he took a step back as he locked his hands behind his back. He managed to meet her eyes then, and she couldn't even begin to hide the tears in them.

"Goodbye, Molly Hooper...for now."

"Goodbye for now, Sherlock."

He looked at her for one moment longer, then turned and went straight to the plane. Molly wondered when, if ever, she would see Sherlock Holmes again.


	5. Series 3 Ep 1

Molly got to work late that morning, rushing to get into the locker room before the manager came down stairs. She was still pulling her hair back as she walked down the hallway, and her mobile rang in her pocket.

"Hi Tom...yep that's fine. Tell them my place. I don't mind cooking. We don't have anything else going this weekend anyway...sure, I'm exited too. Ok, I'll see you later. Ok, love you too, Bye." She stuck her phone back in her lab coat pocket as she approached the locker room.

Molly came in and was ready to start her usual routine. She opened her locker and put her hand bag inside. She had put her hair up on the move, so was also going to check in the mirror to make sure things looked ok. She lifted her eyes, and he was the first thing she saw...

There he stood, just as she had imagined him about a million times over the past two years. But she knew this was real when she whirled around and there he still stood. She stared with mouth agape for a moment and his lips curled very slightly in a small smile. She stood frozen, so he advanced closer to where she was.

"Hello, Molly." The sound of his deep voice echoed in her ears, making her then cover her mouth with a hand as she caught her breath. The reality of his voice was what made it sink in. She could always picture him easily in her minds eye. But his voice seemed to throw her...she could feel it as much as she could hear it.

"You're back...are you really back? I mean, back from the dead? Who knows you're here?" she sputtered out.

"I am indeed back from the dead. I've seen John, and soon everyone in the city will know."

She used her hands to reach down and feel the bench so she could lower herself. She couldn't bring herself to actually look away from him when it had been so very long. Sherlock came over and sat on the bench as well and looked over at her silently.

"It's really you," she said, stating the obvious and narrowing her eyes as she examined him.

"Yes Molly, It's really me." For a heart stopping moment, he reached over to her hand which rested on the bench, and covered it with his own. But he removed it quickly.

It was a touch, just a touch. But it was also enough to completely remind her, and bring her back. She hadn't seen him, heard him, or touched him in two years. And now, all at once, her senses were full of him again. She had begun to tell herself in the last six months or so that she was truly different now. He didn't occupy her mind or disturb her sleep anymore, and she had stopped getting teary at strange moments. But it was over now, and he was back. She found herself right back with him where she feared, and also hoped, she would be again some day.

"I just can't...I can hardly believe it. I was beginning to think you were never coming back. I figured you had started over somewhere else."

"Start over somewhere else? That would be horrible! Where else could I be but here? I was always coming back, Molly. If it took me ten years I still would have come back!" he said in total disgust at the rest of the locations in the world.

Molly's mind began to race. What to tell him...she couldn't think where to begin. So much had happened in two years. So much had happened just recently. She fiddled with her hands, and was reminded that her ring was still being sized...and she found herself breathing a sigh of relief. Then she thought how stupid that was. What did she think? That she'd forever be able to hide the fact that she was getting married? She knew it would come out, but somehow the idea of bringing that up at this moment was completely unthinkable. She was sure Sherlock hadn't come back with any hopes, but it still sounded like a betrayal in her own mind to announce right now that she was engaged.

"Well, I'm glad you're back. We've all missed you of course. Me...and all the dead people," she said with a nervous laugh. "Are you safe now? I mean did you do what you hoped?"

"My work is mostly done for now in that department. My brother was the one that pulled me back here because I was needed on an urgent case. Some sort of terrorist plot going on and they can't seem to figure out who's behind it. I'm actually surprised they managed to last this long without demanding my presence!" he scoffed.

"How did we all manage without you, Sherlock Holmes?" she said shaking her head in mock disbelief. Though if she was honest with herself, the question wasn't sarcastic.

"I wanted to come see you before things got to the newspapers. I'm sure the story will be out by late tomorrow. The last thing I wanted was for any of you to hear it from the news. I almost came to see you first...but then I thought better of it. John was infuriated enough to learn of my being alive all this time without telling him. It would have been all the worse if I hadn't revealed myself to him right away."

"How is he? I mean, I only saw him a couple of times in the past two years." She didn't say that both times he had looked a lot like he had been the one who jumped off a twelve story building.

"He's...engaged it so happens," Sherlock said, sounding a little uncomfortable with the words.

"Is he? Well...lots has happened hasn't it?" She cleared her throat. "Is she nice?"

"I think she's...perfect for John. I don't know much about all of that, but from what I can see it seems a perfect fit. I'm happy for him. I only wish he could perhaps forgive me some time in the next twenty years. I had no idea he would take it so hard!" he said in disbelief.

Molly laughed a little. "Sherlock, you're his best friend. What do you expect? I'd have punched you right in the face if I was him!"

"Hmm, well perhaps a reaction involving physical harm was normal then. I felt he was being awfully dramatic!"

"He'll forgive you. But you'll need to be patient. You can't expect things to suddenly go right back to the way they were years ago. That's not fair. It's not all about you...no really, it's not," she said shaking her head for added emphasis.

His brow was furrowed as he digested this. "And what about you, Molly Hooper? Are you ready to be the consulting detective's pathologist again? Or do you also require some sort of...adjustment period?"

She smiled at him slowly. "Sherlock, I don't think I ever really stopped being the consulting detective's pathologist. I just...had a really long holiday. And to be honest, I'm pretty glad it's over now."

He smiled widely back at her in a way that she rarely got to see, and hadn't seen in years of course. "Well then...I'd say it's time to get to work." He got up from the bench and headed toward the door.

Molly began to lift herself, but found that her legs were absolute jelly, so she stayed where she was. Sherlock turned toward her again before leaving the room.

"I'll be in touch, Molly. It's good to be back." He smiled again, and then he was gone.

But he wasn't gone, she thought. He was back. Back in the city, and back in her life. She laughed at herself now to think that she had managed to convince herself she didn't care anymore if he ever came back. It was a ridiculous notion in hind sight. She hoped she never had to feel such a loss again.

But then she remembered, that in a matter of months, she would have to feel it again. And this time, in a way, it could be worse.


	6. Series 3 Ep 2

It hurt. She had no right to be hurt by it, but it hurt none the less. This woman who stood beside her shooting adoring smiles at Sherlock, and catching the flower that he threw. Where had she come from anyway? He'd known her all of four hours. Sure, she was beautiful and had an attractive personality, but how could he be so comfortable and casual with her? They seemed to hit it off immediately. It was tormenting Molly, and she was terribly distracted by it. It had been bothering her the whole wedding through, but now most of all.

She sulked off away from Jeanine and went to dance with friends since the music had started now. Sherlock was where he should be when she looked over though; talking to John and Mary. She told herself to forget about it, forget everything, and just try to have a dance and enjoy the rest of the night. That worked for maybe one minute.

The next time she looked over, she saw John and Mary dancing happily, and standing not far off was a very lost looking Sherlock. She saw him eying Jeanine in the crowd of guests on the dance floor, but he seemed to change his mind quickly. He made his way past the crowd of people back up to the stage where he had just played for the happy couple. He folded the sheets of music carefully and placed them in an envelope on the music stand. Then he just walked off the stage and through one of the side doors, taking his coat with him from off the back of a chair at the head table.

Again, Molly tried to look away and keep smiling and laughing with the other guests who were totally unaware of what she'd just observed...this time she couldn't even last a minute. Molly excused herself quickly and glanced over to their table where Tom was involved in conversation with one of the ushers. She made her way quickly out the side door where Sherlock had just left.

She saw him still walking along the path that would head through the trees to the parking lot. She wondered what she thought she was doing as she walked quickly to catch up with him. She was engaged, she knew it...and he knew it too. She'd had little to do with Sherlock since the day she'd helped him on the underground terrorist case. He came into the hospital every so often, but it seemed less frequent than before. And the visits were pretty brief as well, and always purely business. She couldn't help but feel that he was trying to keep a bit of distance. Perhaps he was being, as usual, the smart one.

"Sherlock!" she called out, before he got so far that the trees swallowed him up. He turned right away and stopped in his tracks as she caught up on the path. "Where are you off to Sherlock?" she asked, realizing this was a stupid question.

"I was...getting some air," he said, and she realized that he was actually embarrassed that he was caught sneaking off from the wedding that he was supposed to see to the finish.

"Oh...I see. Silly me, I thought you were leaving. I didn't want you to go before I congratulated you on a job well done."

"Oh, you mean saving the Major?" he said, eyebrows raised and expression perking up.

Molly frowned. "No, Sherlock. I meant being best man. You were the _best_ best man I've ever seen, truly. Maybe you should start a consulting best man business on the side." She offered a smile, trying to lighten his mood.

He barely moved his mouth, but glanced back toward the reception building briefly. Then he looked back toward Molly. "I appreciate the thought, but crime solving is far more interesting and surprisingly much less exhausting than the business of weddings. Well I seem to be out here now, so I may as well head home."

"Wait, wait!" Molly said grabbing his arm as he tried to turn. "You cant just leave now, not yet. The party's just starting. You haven't gotten to the fun bits yet!"

Sherlock rolled his eyes. "Please tell me you're not also suggesting this disgusting tradition involving the best man and the maid of honor engaging in some sort of physical-"

"No!" she cut in loudly. "No, I really was not suggesting that. Not even close."

There was an awkward silence for a second before Molly cleared her throat and continued. "Actually I just meant dancing. You should have at least one dance before you run off. I even thought perhaps...we could have a dance." She swallowed as the last words came out.

Sherlock peered down at her in the dim light, looking the way he did when he had deduced her in the past. And it made her nervous. She considered turning and literally running away at that moment because she was afraid of what he would see if he looked close enough. But she also reminded herself that this was Sherlock, so he wasn't likely to see what she was afraid he would. His gaze was interrupted because he looked up past her, back toward the reception. His attention was drawn, clearly because he heard the soft and slow change in the music.

He looked back toward her again and took a breath before responding. "What about Tom?"

"Tom? Oh, he's not dancing right now. He was talking to an usher last I saw. Not really big on dancing anyway!" she said with a shrug.

"And he wouldn't...mind?" Sherlock pressed, narrowing his eyes.

Molly smiled a little. "Why should he mind? You and I, Sherlock, we're old friends aren't we?"

He considered this, then pursed his lips and exhaled. "Well, one dance I suppose...since I practiced." He began walking in step with Molly, back toward the building.

"Stop here," he said though, as they were a stones throw from the door. "The music is loud enough through the open windows and the floor is much too crowded in there with a massive amount of inept dancers."

"Oh, ok," she said, not in a million years considering arguing with him about this.

She'd been touched by Sherlock at times before of course, on a few select and lovely occasions. But only a brief touch of his hand, or a quick kiss on the cheek. There was a different feeling, dancing with a man. It was more like he was holding you. And Sherlock had certainly never held her before. So she tried to relax herself so he wouldn't notice that she was actually shaking a little, as he placed his right hand around her back and took her hand with his left. It had been true when she'd told Sherlock that Tom wouldn't mind. But if he knew what she was feeling in this moment...he surely would.

Although the thought of Sherlock dancing had at first seemed so bizarre to Molly, she quickly realized that there was a reason Sherlock was so good at it. Dancing was a science. It was something that could be measured and timed and perfected, and he liked those sorts of things.

"You have practiced," she said in a complimentary tone.

"I certainly needed to. It had been a long time."

Molly caught him glancing back into the reception hall and saw John and Mary swaying happily together on the dance floor. He almost smiled, but it seemed he couldn't quite manage it.

"The good ones don't disappear you know," she said.

"What?"

"The really good friends I mean, who get married. They don't just get married and then never see you again. John won't do that."

Sherlock seemed to consider this. And he clearly wasn't convinced. Sherlock liked things as is, and didn't do well with change. So Molly realized how difficult this was. Even if he did still have his best friend in some capacity, the life that they had had years ago would never come back. And there was no way to get around that fact. He didn't seem to want to discuss it, because he sort of changed the subject.

"So you don't plan to disappear then, Molly?"

She swallowed hard before replying. "Well, I'm sure I'd still see you all. I don't really know though...you see, Tom was looking at a house in the country about an hour from London. Some friends of his are selling."

Sherlock frowned. "That'll make commuting extremely difficult for you, wont it? You'll be better off taking the train surely. Probably not as long."

Molly looked up nervously. "Well, if we did buy that house, I'm sure I wouldn't be working at Bart's anymore, Sherlock."

His eyes widened as he replied. "You would leave Bart's? But, how could you do that? We need you here."

"You mean you need free reign of the morgue and the hospital lab?"

"Yeees," he said, indicating the obviousness of that answer.

"Well I'm sure you can win over the next employee they find, Sherlock. You'll need to brush up on those flirting skills."

He didn't acknowledge this remark, but continued on. "But what if they aren't as smart as you? What if they don't offer to get me coffee? Or come in on their time off?"

Molly rolled her eyes. "Sherlock, you'd manage." She realized it came out sounding more somber than she'd meant it to.

He narrowed his eyes as he examined her face. "You're sad...Molly, you love working at Bart's. You don't want to leave, do you?"

She barely could look up at him, but couldn't manage an answer.

"Molly, are you...happy?"

"What?"

"Are you happy...with Tom?" he pressed.

She felt her breath speeding up and she was sure that if Sherlock looked at her chest he'd see her heart thudding as hard as she could feel it. Being Sherlock, he really would notice.

"Um, sure. Course I'm happy with him...he's nice," she managed.

"You're lying," he said immediately.

"What? No, he is nice!" she said defensively.

"Oh yes, yes, I realize he's nice." His voice lowered. "But you're not happy with him."

Molly could only concentrate on her breathing at this point and stare at him in something like horror. She realized that the song changed and instead of keeping up with the waltzing, they were now simply swaying with this next soft music in the more modern fashion of slow dancing. She prayed he wouldn't go on, but he did.

"I've never been any sort of expert on matters of the heart, but I feel I can speak with a little more conviction and understanding than I've had in the past. Now that I've known John, and I've known him with Mary. Look at them." He nodded toward the two of them, now sitting at the head table leaning in closely to each other and laughing softly. "Those are two people who love each other. You can see it. They want nothing in the world but to be together. Yes, they may each have their own ambitions and interests, but it's the love of that other person that really keeps them going. I can see now so clearly what that's like, by watching them."

Sherlock looked back down and met Molly's eyes with his own. "That's what you should have too, Molly. You should be just as happy with Tom. And if you're not...don't marry him. Don't just settle for something that you don't really want."

Molly was on the verge of tears by now. And now she was sure he would be able to feel her trembling. She took a shaky breath before answering in a whisper. "Don't...say that to me Sherlock. That's not fair. You can't say that to me." She shook her head a little as she had to look away from his stare.

"What did you say we were before, Molly? Old friends? Isn't it a friend's job to offer some sort of concern or advice?" He sounded a little confused.

"_You_ of all people, of all my friends, can't say things like that to me," she repeated.

"Molly, of all the retched things I've said to you over the years...and this is the one thing you find I'm not allowed to say? Why, Molly?"

She looked at him again with glistening eyes as she answered in a hushed but charged voice. "If you can't understand why it is I don't want to hear that from you, you are not the clever detective that I always thought you were. You know what makes me happy, Sherlock Holmes. You know what I want." She felt his steps falter for the first time since they had begun dancing. "And I can't have it. So don't tell me that I'm not allowed to settle for the nice man who actually feels something for me."

Molly took her hand out of his and stepped away from his hold on her waist. She turned around, looked into the trees, and folded her arms around herself. She wasn't exactly angry with him, but she just had to look away...because it hurt too much. There was silence for a while, but she could tell he was still standing there, not moving as well.

"Molly...I didn't realize. I mean to say, I didn't think that you still...forgive me." His words trailed off, and there was more silence before he tried to speak again. "Two and a half years ago, I hoped you understood that I had to- I had no choice but to go away. There were things that had to be done if I was ever to come back to my life here."

"I know that, Sherlock, but that's not the point." She turned to face him again. "Can you really tell me that things would have been so very different if you had been able to stay? Because I don't think they would have been."

He stared back at her, his eyes piercing blue in the dim light from the reception hall. He started to open his mouth, but then pressed his lips closed again and looked away.

"Right...well, anyway, I appreciate the concern, Sherlock. I'm not angry, really. It's just...hard, that's all." She came over to him again and pressed a quick kiss to his cheek. "Thanks for the dance. I've always wondered what that would be like."

When she pulled back, she saw that he had pressed his eyes closed and slowly began to open them as she turned away. Molly couldn't handle any more. She went to the door and let herself back into the reception. When she shut the door, she looked back out and saw that Sherlock was halfway down the path and pulling his coat up over his shoulders.

At least, she thought as she wiped a tear away, perhaps this could be some sort of closure.


	7. Series 3 Ep 3- Part 1

Molly climbed the stairs to her flat and heard Toby meowing insistently as she neared her door. She mumbled, "I'm coming, I'm coming," as she rummaged in her pocket for her keys. She was also trying to juggle two bags of groceries with her purse. She was just beginning to unlock her door when she nearly jumped out of her skin at the sound of a voice in the dark next to her door.

"Took you long enough, Molly."

"My God! Sherlock, what are you doing here? Why are you leaning on the wall like that?" He moved slowly over to her and she saw that he was not looking very well.

"Of all the days for you to get groceries after work," he continued to complain as he stepped into the light by her doorway. She unlocked her door quickly and threw the bags inside.

"John was looking for you today. He said you left the hospital...did you run away?!" she said as she closed the door behind them and got a better look at him in the light of her flat.

"You make it sound like I'm a child running away from home...I have important things to do which cannot be done in the confines of a hospital bed. Ah!" He collapsed onto her little couch with a groan, lying down on his back.

"Was one of them to come to my place to take a nap on my couch? Honestly, Sherlock, I helped you fake kill yourself once. I refuse to be a part of you killing yourself for real!"

"I came here just for the night. Tomorrow I'll be on my way and out of yours...I'll also require some pain management." He winced again. "It's been six hours since my last dose."

Molly rolled her eyes and crossed her arms. "Sherlock, if you think I'm going to give you anything after the stunts you've pulled recently...there's no way." She sat down on her coffee table in front of the couch.

"Molly, trust me, I do actually need it now. In case you hadn't heard, I was in fact shot two days ago." He turned his head to look at her in a quizzical way. "Had you heard I'd been shot?"

"Yes, though I only heard yesterday, and you were already fine by then...I hadn't been able to come see you yet. Sorry, I just couldn't. I'm afraid I'm not as good at dealing with people who are sick or hurt. It makes me nervous, like I'll do something wrong. Guess that's why I'm better working with the dead. How badly can I mess up really?"

"I don't know, Molly, you seemed astoundingly helpful when I was shot and dying," he mumbled.

"How could I have been-?"

"Nothing, never mind...look, I'm in searing pain, Molly. Care to take my pulse or check my blood pressure or something? What do you think, I have to fake my pain two days after a bullet tore through me? As I recall you have supplies for wounds from one of my previous stays. Will you be able to change the dressing?"

"Oh, alright alright. One thing at a time, Sherlock. I'll get you something for the pain, but I'm keeping it with me! And you don't get any without my permission. I'll certainly be counting the pills ahead of time too. Just try to relax here. I'll look at the dressing after you're more comfortable."

Molly gave him a moderate dose of narcotics and sat with him for a little while to make sure it began to take effect. She could see his breathing slow to normal soon and his face relax.

"You're not off to do something stupid are you?" she said, deciding to break the silence. He was looking almost too comfortable.

"Pfft! I don't do stupid things, Molly. I do, on the other hand, do important things. I have some important business to take care of when I leave here tomorrow. I've got to deal with the shooter."

"What?!" she exclaimed in horror. "They shot you once, Sherlock! What makes you think they wont do it again? And this time finish the job!"

"She wont shoot me again, Molly. I know she wont. But she's got to be dealt with."

"She? A woman shot you? A woman you know?"

"Molly, I can't tell you everything right now. It's probably best you know as little as possible."

Molly crossed her arms in front of her and sat up straight. "Well I don't think that's a very good plan at all. Because if I don't know everything, I'm not giving you anything else for the pain, and I'm not letting you leave. I'll call the hospital if I have to. Or I'll...use force."

Sherlock pushed himself up on his elbows and raised his eyebrows at her. "If you had not recently given me something close to the severity of second degree burns on my face, I would likely be able to laugh off that threat. But, as it is, I imagine you're frighteningly serious...and you have the drugs. Therefore, I will yield."

Sherlock spent the next hour relating to Molly all that had transpired between himself and Magnussen, and then what had happened with Mary as well. He also detailed why he knew full well that Mary had made sure Sherlock did not absolutely have to die that day, and why he needed to tell John the truth, but also pave the way to bring them back together again. He found himself leaving out the bits about Jeanine, but it didn't do much good since Molly was the one that brought her up.

"Jeanine's having heaps of fun at your expense in the media. I half expected you to say she was the one who shot you."

"Well...that probably would have been understandable. I was slightly dishonest about my intentions during our brief relationship. She would have failed to mention in all the interviews that she worked for Magnussen in the private area of his office building. And I confess I found that rather...enticing. She of course was made to believe I found other things more enticing."

Molly covered her face with her hands briefly, then slid them away trying to wipe the images from her mind.

"Sherlock, that's horrible. That's loads worse that giving me fake compliments to get your way at the hospital."

He looked a little injured. "I never gave you fake compliments. I just said things that happen to be true at times when it was the most useful to me. And I wouldn't loose sleep over Jeanine. She's making a killing dragging my name through the mud, and I highly doubt her feelings were really deeply hurt. I don't think I would have had the nerve to do it if I believed she was truly in love with me."

"Well anyway, I'm horrified about Mary, and John. Poor John! God, how many times is that man going to be hurt? I hope you're right about her. I'd like to think they can still be happy. When this is all done. What about Magnussen though?"

"As strange as this may sound, I haven't gotten that far yet. His home seems to be the key, that's all I know. I had one other theory, but that's been disproved. I'm not sure I can talk much longer, Molly. I may need to sleep for a while." She could hear his words becoming a bit more blurry than normal.

"Ok. Come on then," she said and reached for him on the couch.

"I can sleep here!" he said in an irritated tone.

"Don't be silly, you're too tall for this tiny couch. Put your arm around me and I'll get you to the bed. You can sleep in my bed."

"Ah! Fine, alright. Wake me if I sleep too long. The dressing will surely need to be changed by then." He managed to push himself up with Molly pulling and supporting him.

She got him over to the bedroom and he was able to walk himself over to fall into the bed, but she came over to him.

"Give me your coat and scarf, and at least take off your shoes. Oh, here I'll do it." She placed his shoes beside the bed and lay his coat and scarf over her arm chair in the corner. She thought to herself that this wasn't the way she had always dreamed of Sherlock's clothing being strewn about her bedroom. But somehow it sill made her feel a little warm inside to see him resting his head peacefully on her pillow, already almost asleep...

* * *

><p>Sherlock came slowly walking out into the dim light of the kitchen at about twelve thirty that night. Molly had been doing some paperwork at the tiny kitchen table, and looked up when she saw him in the doorway.<p>

"You slept for four hours. How do you feel?"

"Better, I think." and he sat down at the other end of the table that was barely long enough to be considered having another end. "You should have woken me earlier though. I'm on a tight schedule." He rubbed his face with his hands.

"I tried once about an hour ago...well I suppose I didn't really try. I went in and looked at you, and I couldn't bring myself to wake you. You were too peaceful. It's not often anyone gets to see the consulting detective without the wheels turning so furiously!" She smiled a little before looking back down at her papers. "Besides, you can't leave till morning anyway."

"Yes, but I don't want to sleep the entire night away. I've been shot, I'm not dead."

Molly smiled without looking up. She hadn't ever sat like this with Sherlock. It was quiet and dark and relaxed. He wasn't talking a mile a minute, or insulting her, or deducing her. He was just...sitting there. But it was Molly who ended up breaking the silence.

"Oh! Let's get that dressing changed." She got up and went to the little supply cabinet in the hallway and took out what she needed. She recalled the last time she'd had to administer some sort of medical attention to Sherlock. It was over three years ago now. He had made a run to her flat when there was a dangerous gang out to get him. Mrs. Hudson had even had to be relocated briefly to her sister's house in the country. Sherlock had a run in with one of the men and was cut badly. He came to her flat instead of the hospital. It was quicker, he had said. And he didn't like to waste time. She had been an absolute mess at the time though. He was the one who told her most of what to do to clean the wound and stop any residual bleeding. She didn't feel very much appreciated by the time he'd left. Despite the fact that he had come to her for help, and she'd given it to him. She pushed the memory from her mind.

"Come sit on the couch, Sherlock," she called from the living room.

He came out and sat down next to Molly on the couch with a bit of wincing, and began unbuttoning his shirt. He tugged the unbuttoned shirt from the waist of his pants and laid it on the table, then leaned against the back of the couch.

Molly could already see a bit of blood coming through the dressing. "You've been moving too much, Sherlock. You've got to stop moving." She carefully began to peel away the gauze from his chest.

Sherlock sucked in a breath through his teeth and moved so she could pull the rest off from around his back. "What am I supposed to do. Sit immobile in a chair and call John on the phone? I can't do what must be done while staying still."

"Well you'll have to be more careful is all I'm saying. Watch for any dizziness, or suddenly extra sharp pain, or a racing pulse too. It could mean you're bleeding internally. And call an ambulance if that happens! You'll have much less time to play with than you'd like to think." She got a cloth ready to clean the area of the wound.

"I thought you said taking care of someone who's hurt made you nervous. I'm not sure I've ever seen you so, relaxed," he said, then squeezed a throw pillow and winced again as she began wiping the area.

She smiled a little while still concentrating on the task at hand. "Maybe it relaxes me to see you in pain, Sherlock," she said with a little mischief in her voice.

"Charming."

When the wound was cleaned well enough she looked at it for a moment, "It's not so bad. I've seen worse. But then I do-"

"Don't say it!" he groaned.

Without really thinking, she reached out a hand and lightly laid her fingers over the bullet hole. She caught a glimpse of his eyes widen a bit in surprise, and then she actually saw as the touch of her fingers sent little goose bumps up his chest and down his arms. And even though she knew that it was an involuntary response to the sudden touch on a person's skin, especially with her hands being a little cool, it was comforting. It reminded her that he was still just a man. He was a human, and whether he liked it or not, he would respond to others in some ways that were beyond even his control.

"I think it's going to heal just fine," she whispered.

He stared back at her at first without saying anything, then he took a breath and cleared his throat. "Were you planning on applying any other sort of dressing? Or am I going to have to walk around London with your hand attached to my chest?" His lips actually curled in a half smile as he said it.

She stifled a little embarrassed smile of her own and finally removed her hand, then reached for the wrappings she'd gotten before and began working on applying them.

"So...Tom," he said in a low voice suddenly, and her eyes shot up to his for a moment.

"Yes...Tom is gone. It didn't work, and I feel badly, but I just...couldn't."

"You ended it."

"Yes, I ended it. Though he didn't seem to put up much of a fuss...probably just as well then." She took a deep breath as she began to use the surgical tape to seal the edges of the bandage around the bullet wound.

"And you didn't love him," he said softly.

Molly tried to keep working on the bandage. She couldn't look up at him right now. She could see that he was watching her face, but she couldn't meet his eyes. She was afraid she would start crying, or say something stupid that she'd end up regretting.

"No. Not really," she said in a whisper. She was a little discouraged when she realized the dressing change was done, and she had nothing left to occupy her hands and eyes. She sat back, laid her hands in her lap, and managed to glance at him with a brief smile. "Well, you're all done."

He just watched her, saying nothing. She wished with all the strength she had in that moment that she could deduce him the way he could her. There were times when she felt she could read him better than anyone, but most of the time he was nothing but confusion to her. He sat back up with some effort and placed a hand on her knee momentarily.

"Thank you, Molly." Then he got up off the couch. "Do you still have a change of clothes of mine here? I know it's been a while."

She laughed inwardly. Normally this wasn't the circumstances that a man would ask that question. But this was Sherlock, so there were no other possible reasons for him to ask that question.

"I do actually. I'm silly enough to have kept them." She went to her bedroom closet. There were his clothes, neatly folded on the top shelf. She brought them out to him.

"Thank you. I'll need to wash up before I leave in the morning."

"Sure, that's fine. The bathroom's all yours. Are you in any pain right now? Do you need anything for the rest of the night?"

"Actually I'm all right for now. I'll take a little something before I leave though. You should get some sleep, Molly."

She felt hesitant to walk away right now and go to sleep. She was almost afraid that he would disappear the moment she closed her eyes. And that was usually what happened when he'd crashed at her place. Except this time she was more concerned for his health and safety.

"Well, ok. I suppose...shall I take the guest room then?"

"No, I'll sleep in the spare bed. I probably wont be sleeping much anyway, so it hardly matters." He'd never volunteered to do that before.

"Oh. Ok, Well, good night then." She turned again before going into her room. "Please wake me if you're in pain. Or anything happens. I'll leave my door unlocked."

He simply smiled in answer, and she then went into her room, and shut the door.

* * *

><p>Molly startled awake to a touch on her arm. She saw Sherlock sitting on the side of her bed. "What is it? Are you ok? What's wrong?" she said pushing herself up immediately.<p>

"Everything's fine, Molly, but I'm going now."

"Really? What time is it?"

"It's about six. I need to get started and arrange everything now."

"Well, do you need anything? I'll get up and-" She began to push the covers back.

"No, Molly, you don't need to be at work for hours. Go back to sleep. The dressing is still fine. I already washed and changed. And I took half a pill too, so I should be ok. Just enough to keep me comfortable but not so much that I'm falling all over myself. I'll be little good to John and Mary if I can't form a sentence"

"Well, good then." It began to occur to her that he hadn't woken her for any other purpose than to tell her he was leaving. She wasn't quite sure what to say now, once she figured that out.

"I'm sure I'll see you soon, Molly." He leaned in to give her a quick kiss on the cheek. She felt her face redden and become hot instantly, but was grateful he probably wouldn't have seen with the light being off still in her bedroom.

Sherlock got up and went to her bedroom door. He looked back and offered a small smile before adding, "Thank you." Then he left. She heard the door to her flat open and close a minute later, and she fell back against her pillow exhaling loudly. She was fairly sure she wouldn't be able to fall back asleep with her mind, and heart, racing like this.


	8. Series 3 Ep 3- Part 2

It had been many months since the night Sherlock had sought refuge at Molly's flat. And she'd seen him off and on at the hospital, as was the case before. It seemed that his efforts since he had left her flat those months before had been rather successful. John and Mary appeared to still be together, and from what Sherlock had told her, John knew everything that he needed to make a completely informed decision. But Molly had then heard some disturbing news about two weeks ago around Christmas.

She didn't believe it at first, and had chalked it up to people trying to discredit Sherlock yet again. But the more she heard in the news, and failed to see Sherlock show up at the hospital, the more she began to think that something had really happened. Could Sherlock have really killed Magnussen? She had ended up texting him, desperate to get some sort of answer. But none came.

It was a week after the news broke that John came by the hospital and gave her the answers she both needed, and didn't really want, to hear. It shocked her. She knew how fiercely Sherlock cared for John and Mary, but had never realized how far he would go to protect them. It changed nothing about her feelings for him, since she knew the truth about Magnussen already. But it did worry her of course. She wondered what would happen to Sherlock now. And John had little information to offer on that front. He didn't know much himself. The people at the top seemed to have Sherlock completely closed off and were preventing any sort of communication. There was no public trial either. Everything was done behind closed doors. So they were all just left to wait.

Molly was trying to keep busy and was involved in some testing at the lab that day, and she was busily recording findings in the computer. She was shocked when she heard a message come in to her phone, and saw that it was from Sherlock.

I NEED TO SEE YOU. CAN I COME TO BART'S? -SH

She immediately sent off a reply.

YES, PLEASE COME! IM IN THE LAB. :) -MH

Molly was almost shaking she was so nervous now. But she was glad. He couldn't be in too much trouble if they were letting him out to visit friends. She ran to the locker room to make sure that she looked ok. She found that she looked pretty much the same as always when Sherlock saw her, so she didn't do anything to herself. It was more of a nervous habit to check her appearance. She came back to the lab and tried to continue working, though she was extremely distracted now.

Finally, she saw Sherlock walking down the hallway followed by two men in uniform. He stopped by the door and spoke to them for a moment, then the men turned and went back down the hall, leaving Sherlock where he stood. Finally he opened the lab door and came in.

"Hello, Molly. It's been a long time."

"Sherlock, I couldn't believe it when I got your message! Is it done then? I mean, the trial. Are you back home?"

He looked at her strangely. Seriously, it seemed like. He seemed to be a little distracted. "Yes, Molly, the trial is over. I'm sorry I haven't been able to communicate with anyone the past couple weeks. I wasn't allowed to."

"Did they have you locked up?"

"Just as bad. I was made to stay with Mycroft. And all electronic communication were taken away from me. It was, by far, the worst two weeks of my life." He looked like he meant it.

"Have you seen John?" she asked a little excitedly.

"I'll be seeing John and Mary in a little while. I just paid a little visit to Mrs. Hudson, and then Lestrade."

"How nice! You're really making the rounds aren't you?"

Sherlock didn't smile, but looked sad. "I am...I'm saying good bye, Molly."

Her face changed then as well. "Wait, what? Goodbye? Where are you going? Are they putting you in jail?!"

"No. But I can't stay here. It seems I've finally worn out my welcome in England. Despite Magnussen's less than lovable qualities, it's apparently still frowned upon to shoot am unarmed man in the head."

"B-but your brother...couldn't he do something?" she stammered.

"He did do something. He kept me out of jail, and that was all he could do. He instead allowed me to be given a far away assignment. A sort of, permanent assignment. I'm going undercover in Eastern Europe."

"You'll be undercover permanently? That's an unusual job."

Sherlock pressed his lips together and locked his hands behind his back as he walked over to where she stood behind the table in the lab. "The job is of such a nature that it will only last about six months. But I wont be coming home when it's done...or ever."

Then he met her eyes...

She'd only seen that look in his eyes once before, and it was when he thought he was going to die. She looked at him harder, searching his face and trying to find something different than what she could already see, wanting so badly to get a different answer. But there was none.

He moved his eyes away from hers. It looked like he was actually fighting back emotion.

"Oh," she said very quietly. "I see."

"Yes well, you can understand now why I'm making the rounds, as you say."

"You may be fine, Sherlock. You've gotten out of worse things than this haven't you?" She knew she was grasping at straws.

"I'm not allowed to get out of this one though, Molly. They don't mean for me to come back. The only favor they're doing me is to give me something to occupy my time...whatever time I have left."

She began breathing heavily and walked away from the table for a moment. She paced back and forth, holding her hand against her mouth. She shook her head a little and combed through her brain, trying to come up with some sort of a solution. Or at least some sort of comfort. She came up with nothing, and she marched back to where he stood.

"You can't go away like this, Sherlock. I just...I can't." She covered her mouth for a moment, then she spoke again. "Did you tell Mrs. Hudson? Lestrade?"

"I didn't want to upset them. They only know I've been given an assignment to take me out of the British government's hair for a while."

She stared at him wide eyed. "You didn't want to upset _them_?" she demanded, sadness turning to fury.

"I wanted to be honest with you...this last time. There is a lot I want to say, and I felt that it would make more sense if you understood why I really need to say it now."

"Because you think this is it." Her voice broke a little. "You think we'll never see each other again."

He made no reply, but didn't need to. She could clearly see this was what he believed, and why he had come to see her. He sighed and seemed uncomfortable suddenly. Sherlock reached up and pulled the loop of his scarf open, placing it on the lab table.

"I don't have a lot of time, so I shouldn't waste any. Actually that's rather the topic I meant to discuss. You see I know that I've owed you many an apology over the years we've known each other. And although it would probably be fitting to express my sincerest apologies for any and all mistreatment you've experienced at my hand, as I leave you for the last time, I feel I'd rather say something a little different. I have told you I'm sorry on several occasions. But there's something I haven't expressed honestly yet...and that's regret."

Sherlock walked around a little, seeming to feel as uneasy as she did. He simply switched to standing at the other end of the table, making Molly turn so she was still facing him. Then he began again.

"There are many things I've done and not done in my life, Molly, that I feel no regret over. I recently killed a man, for instance. I feel no regret over that because of my reasons for my doing so. But, even so, there are a select few things I do regret." He took a step closer to Molly before continuing softly. "When I stand here with you, Molly, I am a man full of regret. I have wasted so much time, simply because I thought I had plenty of it. I find now that my time has very suddenly run out. I cannot say for absolute certain whether I would have been able to love you, Molly Hooper, the way that you so constantly and unconditionally love me. But I can honestly say that I wish I could have had the time to try. I regret that I never got the chance to fall in love with you."

Molly was completely covering her face by now, trying to hide the tears that were falling. "Why would you do this to me now, Sherlock? My God! Couldn't you just sneak off and pretend you never cared about me?" she mumbled through her fingers.

"I am sorry. I had to say it. I felt this was the least painful option. I know you've questioned what my feelings actually were since my return from being away last time. And I imagined that you would forever question that, if I was...gone, and had never told you the truth. I know I can't handle the rare moments when I have no answers. I assumed that it would bother you as well."

Molly wiped her face with the sleeve of her lab coat, then took a deep breath while pointing her face to the ceiling. She looked back at Sherlock with her red eyes.

"Are you pretending? Is this some sort of grand gesture that you think you should offer me since it'll never come to anything anyway? I mean, you almost let me marry Tom! And you said nothing about any sort of feelings!"

"I didn't know what exactly to do about that. I felt that you had wisely moved on while I had been away. And I believed at first that you were happy. I could have lived with that...but when I got a clear indication, at the wedding, that you were not in fact happy with Tom, I spoke honestly, because I cared, Molly. When I found that you still felt much the same as you had years ago, I did what I always chose in the past when it came to you. Nothing. I have no excuses except what I had said before. I always believed I had the time. Somewhere in my head there were plans for...something one day...for us perhaps. But now I'm forced to realize that day won't be coming. There's nothing I can do to change that now. All I can do is confess and hope that it offers some sort of comfort to you."

Molly felt like she'd been hit by a train. Her tears had stopped, and she just felt tired. She had never imagined a more horrible way for Sherlock to tell her that he cared for her. She had tried to think of scenarios many times, but never had come up with something so awful, for herself, and for him also. He was hurting, and she could see it. She was angry with him in a way, but as usual, she certainly didn't want to see him in pain.

"It helps, Sherlock...it does," she said softly.

He still looked sad himself, but drew a breath and straightened up again before speaking. "I had of course carefully planned out what I wanted to say to you today, and I had accounted for all possible reactions on your end. You were, by the way, at the happy medium of reactions I had anticipated. And I'm pleased that you neither physically threw yourself at me, nor began to throw implements of research at my head."

At this point Molly snorted out a laugh then covered her mouth, and thought she even saw him crack a smile before going on.

"I also agonized on one other point in particular. In addition to being honest about my feelings verbally, I had thought a lot about whether or not I should kiss you before I take my leave." He looked at her pointedly.

Molly had to now close her mouth which was hanging open. She stared back at him, wondering what she was supposed to say to this, but then he went on.

"I realize, along with the pain that my honestly could leave after I'm gone, kissing you could certainly leave a sting of emptiness that you wouldn't have to know if I were to simply leave you without such an intense and physical show of affection."

She raised her eyebrows, wondering if this was in fact his final answer to the apparent conundrum, but then he spoke again.

"But..." He stepped even closer. "I also felt that, for lack of better words, I owe you something. I can't turn back time and make up for the things I should have done in the past. But I can at least avoid doing the very same thing again."

"You're saying you owe me a...kiss?"

"Well, I'm sure I owe you more than that...but do understand I only have a couple of minutes." He smiled.

She couldn't help smiling too, despite her sadness. Molly reached over then, and grasped the front of his coat in both her hands and tugged him forward a little, closing any distance left between them. "Only a couple more minutes?" she questioned, and he nodded. "Then, Sherlock...do shut up and start kissing me."

Sherlock grinned, in that rare and beautiful way, as her reached down to hold Molly's face between his hands. He brought his face down, hesitated for a second just before he reached her, then pressed his mouth to hers. He had seemed unsure at first, but his lips soon parted in order to taste hers more perfectly. And then any trepidation melted away as the two people who had been separate so very long, molded together in only the time it took for one breath.

It was of course bitter sweet. This kiss, for Molly, from the man that she loved so much and for so long, was the most moving she had ever experienced. It was physically moving of course. But she also felt a depth of passion that she hadn't realized was possible in Sherlock. Not just with her, but maybe with anyone. She felt longing, and sadness, and fear, and regret all through the connecting of his mouth to hers. She didn't realize that her tears had begun to fall again, until he finally pulled his lips from hers.

Sherlock's eyes were squeezed together as he took a breath deeply and pressed his forehead against hers. "I'm sorry...that was meant to be for you," he whispered.

She looked at him and let out a shaky laugh. "Wasn't it?"

"I thought it was for you. I thought that's why I did it...but I wanted to kiss you. I just didn't realize how much till I actually did it." He slid his hands away from her face and wrapped them around her body holding her tightly. Molly did the same and pressed her face against his neck. They stayed like that for a moment, then they heard the knock on the door.

Sherlock turned around and saw the two men standing there waiting. "I've got to go," he said simply, and put his typical serious looking expression back on. He gently grasped her face again and quickly kissed her lips before turning and walking to the door. Molly ran to follow him.

"Wait! Sherlock wait! Just- promise me you'll try to come back," she said holding him from the door by his arm.

"Molly," he began somberly "The chances of my safe return-"

"Shut up, Sherlock!" she instructed while raising her hand to halt his words. "I love you, and I'm asking you to promise me you'll try...please."

"All right. All right, Molly, I'll try to come back...promise." She could see that he meant it, no matter how unlikely he felt his chances were. Then Sherlock turned his collar up on his coat.

"Goodbye, Molly Hooper." He opened the door and walked out, immediately heading down the hall with the two men...and disappeared.

Molly slid to the floor and cradled her face in her hands...

* * *

><p>About an hour later, Molly peeled herself from the floor of the lab and trudged over to the table. She had hours left of work and nobody to cover for her. So she figured she'd better just stop feeling sorry for herself and go on with life. What else was there to do? She'd probably never see Sherlock again, so she figured she should concentrate on putting one foot in front of the other and carrying on. At least she could turn him into a lovely memory, instead of a regret.<p>

She finished up the rest of the report quickly and then decided to walk down the hall to drop it on her manager's desk. By the time she came back to the lab, she was in absolute shock...because she had passed a television along the way.

How was it possible? Could Moriarty really be alive? Had he faked his death much the same way Sherlock had? Or was that even him who had confronted Sherlock on the roof that fateful day?

She gave a little yelp and jumped, not long after, when she heard her mobile vibrating along the top of the lab table. She dove to answer it when she saw it was Sherlock.

"Hello, Molly."

"Sherlock! Did you hear the-"

"Yes."

"How can he be-"

"Molly, I called to repeat what I had expressed. My feelings are truly what I said they were when I saw you before. I didn't say it simply for your benefit, or because I thought I'd never see you again. If I were to see you again, I would be glad to continue exactly where we left off."

"Yes, I know, Sherlock," she said softly, and began to smile.

"Where are you?"

"Oh, um...I'm still at work. I'm still in the lab...are you in the air then?"

"Not exactly...Molly, can you come out into the hallway?" he asked, his voice low and soft.

Her heart absolutely halted. She couldn't even form a response. She didn't want to ask why or what he meant, because she was too afraid of what the answer could be. She didn't want to hope, but didn't want to ruin any hope either. She simply walked to the lab door and stepped out into the white hallway and turned...

Sherlock stood a few yards away holding his phone to his ear. He lowered it slowly and hung up the call, placing the phone then in his pocket. And then he began to smile.


End file.
